Aquavetplan enterprise Manual Version 0, 2015

Section B Industry sector information

System definitions Error: Reference source not found

B1 Open systems Error: Reference source not found

B1.1 Introduction Error: Reference source not found

B1.2 Catchment Error: Reference source not found

B1.3 Estuarine Error: Reference source not found

B1.4 Marine Error: Reference source not found

B2 Semi-open systems Error: Reference source not found

B2.1 Overview of semi-open systems Error: Reference source not found

B2.2 Southern bluefin tuna net-pen culture Error: Reference source not found

B2.3 Salmonid net-pen culture Error: Reference source not found

B2.4 Barramundi grow-out Error: Reference source not found

B2.5 Yellowtail kingfish net-pen culture Error: Reference source not found

B2.6 Pearl oyster culture Error: Reference source not found

B2.7 Edible shellfish grow-out Error: Reference source not found

B3 Semi-closed systems Error: Reference source not found

B3.1 Overview of semi-closed systems Error: Reference source not found

B3.2 Native freshwater finfish Error: Reference source not found

B3.2.2 System inputs Error: Reference source not found

B3.3 Prawns for grow-out Error: Reference source not found

B3.4 Prawn hatcheries Error: Reference source not found

B3.5 Trout in fresh water Error: Reference source not found

B3.6 Salmon hatcheries and raceways Error: Reference source not found

B3.7 Marine finfish hatcheries Error: Reference source not found

B3.8 Freshwater crayfish Error: Reference source not found

B3.9 Abalone Error: Reference source not found

B4 Closed systems Error: Reference source not found

B4.1 Overview of closed systems Error: Reference source not found

B4.2 Ornamental aquatic animals Error: Reference source not found

B4.3 Native freshwater finfish Error: Reference source not found

System definitions

Systems are defined by the degree of control over movement of water and animals. They vary from open systems (e.g. wild fisheries), in which there is no control over movement of water or animals, to closed systems (e.g. closed recirculation systems), in which there is complete control over movement of water and animals. Characteristics of these systems are summarised in Table 1.

Table 1 Characteristics of aquatic animal industry systems

System	Water movement containment	Animal movement containment	Examples
Open	No	No	Wild fisheries; ranching
Semi-open	No	Yes	Net-pens, cages
Semi-closed	Partial	Yes	Ponds, raceways
Closed	Yes	Yes	Recirculating systems; aquaria

B1 Open systems

B1.1 Introduction

Aquatic animal disease emergencies occurring in open waterways will be very difficult to manage because of the variety of animals present in these systems, uncontrolled movements of aquatic animals and the waters in which they live, and interactions with people who use the waterways. If diseases and pests become established in an open system, control options are very limited. Eradication from the environment may not be an option.

This section provides information on fishing industry practices, which will be useful in deciding:

• 
  whether control measures are warranted in open systems
  
• 
  which control measures could be used
  
• 
  how to implement the control measures.
  

This section does not describe individual fisheries in detail. Individual Australian fisheries are described elsewhere (e.g. in FRDC 2003).

Information is provided on the types or species of animals in fisheries based on open systems (i.e. pelagic or demersal finfish, or crustaceans) and the types of technology involved in their capture (e.g. longline, trawl, pots). Information is also provided that will be useful in designing a disease control program. Section C details possible management strategies in open systems.

B1.1.1 Overview of open systems

Open systems are waterways in which there is little, if any, control over movement of animals and water. For control purposes, water and animals cannot be contained.

Open systems cover a diverse range of environments in fresh, brackish and salt water, and provide habitat for a vast array of animal species. Within these systems, a broad range of human activities take place, including commercial and recreational fishing, and other commercial and recreational pursuits.

Because of their complex nature, open systems have been separated into three broad categories:

catchment includes lakes, impoundments and river systems

marine refers to the oceanic environment

estuarine refers to the transitional zones between catchment and marine.

Open-water commercial fishing industries comprise:

• 
  those managed by the state and territory governments (through their fisheries departments): coral reef, coastal marine and estuarine fisheries for finfish, shellfish (crustaceans, molluscs) and ornamental fishes
  
• 
  those managed by the Commonwealth through the Australian Fisheries Management Authority (AFMA): marine deepwater trawl, scalefish, billfish, tuna, shark and scallop fisheries.
  

Open-water non-commercially fished waterways include:

• 
  many freshwater lakes and estuarine fisheries in the mainland states and Tasmania
  
• 
  some large lakes of the scale of Lakes Awoonga, Eucumbene and Jindabyne.
  

Although these areas can theoretically be closed off, their size means that they are more appropriately regarded as open systems. Stocked farm dams and the smaller commercial impoundments, where the discharge water could be contained, are considered semi-closed systems (see Section B.3).

Open-water aquaculture operations include:

• 
  restocking and reseeding of molluscs (scallops, clams, trochus, oysters and abalone)
  
• 
  ranching, which may involve aggregating fish (e.g. snapper) around feeders and artificial structures. Fish may have been stocked into the environment or may be attracted to the area. Some ranching may involve private ownership of stock (where the stock has been produced in aquaculture and released into a defined area). Ranching is not yet a preferred farming method in Australian waters but could grow in popularity.
  

Within these open systems, there are four main groups of animals:

• 
  animals that form the basis of commercial and recreational fishing industries
  
• 
  animals that have been restocked for fisheries or conservation/restoration purposes
  
• 
  animals that comprise the remaining ecosystem fauna of the open waters of Australia
  
• 
  animals that are farmed (in semi-open systems—see Section B.2), are within an open system, and include both native and introduced species.
  

B1.1.2 Controlling diseases and pests in open systems

Diseases and pests are difficult, if not impossible, to detect, manage or eradicate in open-water systems. Complex interactions of novel (including exotic) disease agents and hosts in open systems may result in disease, which may be transmissible to native species or new hosts, with potentially devastating results. However, this complexity means that not all exotic disease agents can be expected to manifest the same disease outcomes under Australian conditions as they display in other countries.

Catchment, estuary and marine ecosystems are quite different, with different populations of important pelagic, demersal and benthic species. In developing a framework for management of disease outbreaks in this environment, it is important to consider impacts at all levels of the ecosystem, as well as on commercial and recreational species. Losses at one level may have significant impacts on the stability of food chains across the ecology of an aquatic environment.

Table 2 provides an outline of the major groups of animals that, at a minimum, should be considered in the development of a disease control plan for an open system. Other animals (e.g. seabirds, wading birds) may also need to be considered if they interact in a significant way with aquatic species.

Table 2 Major aquatic species groups in open systems that should be considered in disease control plans

Life cycle behaviour	Habitat type
	Catchment	Estuarine	Marine
Mobile migratory	Finfish	Finfish, crustaceans	Finfish, crustaceans, cephalopod molluscs
Mobile territorial	Finfish, crustaceans	Finfish, crustaceans	Finfish, crustaceans, cephalopod molluscs
Semi-mobile	Finfish, crustaceans	Finfish, crustaceans, echinoderms	Finfish, crustaceans, echinoderms
Sedentary	Crustaceans, molluscs	Crustaceans, molluscs, echinoderms	Crustaceans, molluscs, echinoderms, corals, live rock

B1.1.3 Interactions between open systems, farmed systems and aquaculture species

Semi-open and semi-closed farming systems interact with open systems and could contribute significantly to the potential for a disease outbreak. Farmed species may also act as indicators of a problem originating from the open system. Sections B2, B3 and B4 provide further information on farming practices in semi-open, semi-closed and closed systems, respectively.

Diseases found in farmed systems have the potential to affect wild animals, and any proposed controls on semi-open systems should include consideration of the potential impact and management on open-water species.

Farmed species with direct (or indirect) contact with open systems include:

• 
  farmed marine or estuarine finfish—barramundi, bream, cobia, estuary cod, kingfish, mulloway, salmon, coral trout, ocean trout, tuna and snapper
  
• 
  crustaceans— lobsters, prawns and mud crabs
  
• 
  molluscs—Sydney rock oysters, Pacific oysters, pearl oysters, other edible oysters, abalone and mussels
  
• 
  other invertebrates—sea cucumbers, sea urchins, corals and live rock.
  

Most farming activity takes place in the intertidal or coastal zone in semi-open systems; although farmed in open waters, stocked animals are contained and managed within the farm environment. Although farming in semi-open systems does not often take place in freshwater impoundments or rivers in Australia, semi-closed systems often use water from these sources, and the effluent then flows back into the waterways. This water exchange means that this type of farming has the potential to transmit disease to or from the farming enterprise. Escaped, released or translocated stock may also be carriers of disease that could be harmful to native aquatic animals.

B1.2 Catchment

Inland catchments have a range of native species, including finfish, crustaceans and molluscs. Many also have introduced species. Some systems are stocked periodically with introduced species such as salmonids, and native species such as Murray cod, trout cod, silver perch, barramundi, Australian bass and golden perch.

The interaction of closed, semi-closed and semi-open aquaculture systems with open systems as a result of restocking activities requires an understanding of the husbandry practices of hatchery operation. Once released, however, the stocked fish are considered as ‘wild stock’ in terms of open system management.

The main potential for disease introduction and transmission in catchments includes:

• 
  deliberate or accidental introduction of exotic aquatic species such as sportfish and ornamental fish
  
• 
  introduction of organisms transported in ballast water or attached to vessels
  
• 
  release of effluent water from aquaculture sites
  
• 
  stock escape from aquaculture
  
• 
  use and translocation of domestic and imported live fish or fish products as bait
  
• 
  movement of migratory birds and wildlife
  
• 
  aquaculture feeds
  
• 
  movement of contaminated fishing (commercial and recreational) or aquaculture equipment
  
• 
  international human traffic and associated fomite vectors (e.g. fishing gear such as waders).
  

B1.2.1 Practices

General use of waterways

The freshwater environment in Australia is used by the general public for utilities, agriculture, industrial uses, some commercial fishing and a variety of recreational activities. Under state and territory legislation, not all freshwater and catchment systems are open to the public. Catchment areas may be closed to the public to conserve the quality of the water for human consumption, and for environmental purposes to preserve endangered stocks of native fish and other aquatic animals.

Recreational fishing

Recreational fishers target both native and introduced species using a variety of hook-and-line fishing methods for finfish, and traps and nets for freshwater crustaceans. Many recreational fishers have boats, and move around and between a number of catchments. Their equipment, which is generally not disinfected, moves with them—in some cases, into international waters.

Recreational fishing includes three main types of hook-and-line fishing activity:

• 
  Flyfishing, predominantly a shore-based activity, involves the use of a long rod to cast artificial flies (lures), made from plastic, animal hair, fur and/or feathers, onto the surface of lakes and rivers. There are two different flyfishing techniques: wet and dry. The main difference is that dry flies are used on the water surface, whereas wet flies sink through the water column.
  
• 
  Trolling, spinning and lure fishing all involve the use of a rod and reel of line to cast an artificial lure into the water, to entice a strike from a fish. A variety of lures are used; most are made from plastics (either hard or soft), wood or fibreglass. Trolling is where the lures are trailed behind the moving boat to catch fish.
  
• 
  Bait fishing involves casting a baited hook at the end of a line. Bait fishers may also throw berley (e.g. pollard, squashed shellfish, minced fish, blood and offal) into the water to attract fish to the area, to increase the chance of a catch. Bait comes in a variety of forms—including worms, insects, grubs, cheese and sweet corn—depending on the species being targeted. Local or translocated native or aquarium fish are sometimes used as live bait; and imported or local fish and crustaceans (prawns) may be used as dead bait. Bait may also be used in traps set for freshwater crustaceans such as yabbies, redclaw and giant prawns (Macrobrachium spp.).
  

Commercial fishing

Commercial fishing activity in inland Australia centres on fishing for carp in the Murray–Darling system, eels in impoundments, and golden cobbler in Lake Argyle in Western Australia. Most other impoundments are open only to recreational fishers or are closed to protect fish stocks. Commercial fishers generally use nets, traps and line fishing methods. For example, eels are trapped in impoundments for export markets. Electrofishing is used in a number of waterways for carp—this involves stunning the fish, which are then scooped from the water using nets.

B1.2.2 Premises and equipment

The equipment used by recreational fishers is described above. Other premises and facilities used by recreational fishers and other users of the inland aquatic environment include camping sites, camping grounds, caravan parks, cabins and boat launching facilities. Fishing boats in inland waters are generally small (less than 6 m), of aluminium or fibreglass construction, and powered by petrol or electric motors, oars or paddles. Craft of this kind are used by both the recreational and commercial sectors. Canoes, kayaks and houseboats may also be used by recreational anglers.

Most fish catches are cleaned either on the boat or on riverbanks, with the offal cast back into the water. The fish are then washed and stored on ice, or frozen in portable cooler boxes. Freshwater prawns and crayfish may be transported live.

In the commercial industry, there are few processing facilities for freshwater fish. In most cases, processing of fish takes place either on the boat or at a shore-based facility. Carp are normally taken whole to be processed in an industrial feed or fertiliser processing facility. Fish that are processed for the domestic market for human consumption must be processed in facilities approved by the state or territory department of health.

B1.2.3 System inputs

Aquatic animals

Natural recruitment of species occurs in most systems, with the exception of some impoundments. In addition, salmonids and native fish are restocked for recreational angling, and for conservation and supplementation of native species. Fish and crustaceans may occasionally escape from semi-open and even semi-closed systems, particularly during flood events or cyclonic conditions.

The native populations of crustaceans, molluscs and eels are self-recruiting. The main possible mechanisms for disease transfer are migration of vectors or secondary hosts (e.g. eels, barramundi), translocation by people of species within their natural range, and introduction of new native or exotic species into a waterway. Translocation may occur for stocking purposes, through the use of live fish or crustaceans as bait, or through release of aquarium fish that are no longer wanted. Migrating eels, which can cover vast distances from the Pacific Ocean to inland waterways, may be carriers of infectious disease agents.

The introduction of fish from different systems can introduce disease if the fish are infected, either overtly (i.e. showing clinical signs) or covertly (i.e. as carriers with no clinical signs). Introduction of a new disease can devastate native fish populations because the fish may be naive, with no natural or acquired resistance to the disease. However, the pathogen will not necessarily establish because local conditions may not be conducive.

Water

The water in catchment systems comes from rainfall or springs. Rainfall water usually runs over land into the tributaries of rivers, or into the lakes or impoundments. As the water passes over the landmass, it picks up bacteria, viruses, chemicals, nutrients and minerals from the surrounding environment. These inputs to the water system may or may not have a significant effect on the ecosystem.

Other inputs to waterways include:

• 
  water from stormwater drains and municipal sewage outfalls
  
• 
  runoff from agricultural and pastoral areas
  
• 
  organic carbon runoff from dead pasture after flood events
  
• 
  waste from domestic livestock
  
• 
  chemicals (pesticides, herbicides and fungicides), fertiliser, runoff from acid sulfate soils, runoff from landfill leaching and aquaculture
  
• 
  chemicals such as hydrocarbons from motor fuel and oil, anti-fouling chemicals, and wastes from boats
  
• 
  sunscreen cream, which has been identified overseas as a pollutant of water in holiday areas
  
• 
  untreated sewage from houseboats
  
• 
  untreated sewage runoff from recreational and camping areas, and from septic systems.
  

Such runoff may affect the health of the inhabitant fish (e.g. epizootic ulcerative syndrome in native freshwater and estuarine fish can be triggered by runoff from acid sulfate soils) or affect human food safety (e.g. via contamination by untreated sewage or generation of algal blooms). Pesticide, fungicide and herbicide use can result in spray drift or runoff into water bodies; these chemicals can lead to a wide suite of acute lethal and insidious sublethal effects on aquatic animal health.

Toxic algal blooms in the Murray–Darling river system have been linked to elevated nutrient levels. Sources of nutrients include municipal sewage outfalls, surface runoff from agricultural land where excess fertilisers are used, and runoff from livestock farming areas. Runoff has also been linked to deoxygenation events in the eastern drainage rivers during flood events.

Feed and bait

Bait and berley for both commercial and recreational activity include live and dead fish, worms, insects, insect larvae, frogs, tadpoles, meat, offal and blood from a variety of animals and birds. For some species, they may also include vegetable and cereal products such as sweet corn, tomatoes, pollard and bran.

Other influences (including personnel, equipment, vehicles and stores)

Personnel in freshwater areas include recreational boaters and fishers, and commercial fishers. Fishers and their equipment can act as fomites for pathogen transfer between waterways.

Commercial and recreational fishers, and the general public need to be educated about the need to advise authorities if fish kills and diseases are observed. This could be through schools, fishing clubs, fishers’ co-ops and local media outlets. Contact points need to be established for information exchange. Nowak et al. (2005) provide an excellent template for fish kill investigation and sampling approaches.

B1.2.4 System outputs

Aquatic animals

Take of fish, freshwater mussels and crustaceans from inland rivers and lakes is limited by both the recreational and commercial sectors. Some, usually small, fish and shellfish may be taken for use as dead or live bait in the same locality or nearby.

Most fish taken are processed for human or pet consumption. A small number of brood fish are taken live for breeding schemes. These are generally taken under licence issued by the state or territory fisheries authority.

Water

The flow-through water in open catchment systems is often used for drinking water. Local public health authorities, or state or territory environmental protection agencies usually monitor water quality. Other monitoring may be done by farmers who use the water for domestic livestock or irrigation, or by local aquaculturists.

Waste materials

Best-practice use of the aquatic environment requires that people remove their rubbish from the area; however, food scraps are often left for birds and other scavengers to consume or spread. Other wastes in effluent water, septic overflows and sewage outflows enter the system from holiday facilities such as camping sites, caravan parks and cabins

B1.2.5 Groups involved in catchment management

Groups involved in catchment management vary between jurisdictions. They include water resources commissions or water boards, catchment management authorities, state or territory departments of primary industries and fisheries, environmental protection agencies, local governments, lands departments, health departments, acclimatisation societies, other recreational groups, farmers and conservation groups.

The Murray–Darling Basin Authority is the multijurisdictional body responsible for water management in the rivers and lakes of the Murray–Darling system.

Snowy Hydro and the New South Wales National Parks and Wildlife Service are involved in catchment management in the Snowy Mountains. In other states where dams have been constructed to generate hydroelectricity, the electricity authorities would be involved.

B1.2.6 Legislation and codes of practice

Legislation relating to the management of catchment fisheries is generally managed by state and territory fisheries managers. The exceptions are fisheries that are managed under the Environment Protection and Biodiversity Conservation Act 1999 by the the Australian Government Department of the Environment, and waterways within national parks that are managed under national parks legislation. The Recfish National Code of Practice for Recreational and Sport Fishing (recfishingresearch.org/national-code-of-practice) applies in all environments.

See Appendix 1 for information on relevant legislation.

B1.2.7 Occupational health

Human health issues may be associated with chemical spills, algal blooms (especially blue–green algae), and infectious organisms such as Cryptosporidium and Giardia. Sewage contamination can lead to infectious diseases such as hepatitis A and enteric viral, bacterial and parasitic infections.

See Appendix 2 for information on seafood-borne disease in humans.

B1.3 Estuarine

Estuaries often have a tidal influence. They are subject to fluctuations in salinity, temperature and other environmental parameters linked to the tides and rates of freshwater flow. Estuaries are often the sites of ports and built-up areas, and may be used for many recreational activities. They are important breeding and nursery areas for many marine and diadromous fish and invertebrates, as well as wetland birds.

B1.3.1 Uses

The most common fishing practices in estuaries are prawning, crabbing, recreational line fishing, shellfish collection and commercial fishing. Aquaculture activities such as shellfish farming, prawn farming and finfish grow-out also occur. Other recreational activities in estuaries include swimming and boating. Estuaries are often ports or anchorages for marine fishing fleets, international cargo vessels and recreational craft, including international cruising and sailing craft.

B1.3.2 Premises and equipment

Both commercial and recreational fishers fish estuarine areas. Coastal fishing fleets, depending on the size of the craft, often travel significant distances offshore to fish and then return to their home ports. Commercial fishers in these areas use a variety of lines, traps, dredges, nets and trawls, depending on the target species (e.g. crabs, prawns, finfish, scallops). Scallop fisheries use dredges to extract scallops from the sediment.

Recreational fishers use a rod and line to target most species, but can also use hoop nets and traps to target crabs, and hand-dip nets and haul nets to capture prawns. Recreational fishers also use boats and dinghies, which often have outboard motors. Estuarine areas have boat ramps where fish captured by recreational fishers from estuaries and offshore locations are often cleaned.

The aquaculture sector has a number of different structures in estuarine areas, depending on the farmed species. Shellfish farms have sheds, racks, trays, punts, sticks and wharf facilities. Fish processing facilities can be large and generate significant quantities of waste. Restaurants and eating areas, which can be located on the water’s edge, can generate processing and leftover wastes.

Camping facilities may be present—for example, council facilities for tents and permanent caravan-type structures, which also may have communal fish cleaning areas.

Also using the harbour and bunkering facilities of coastal ports and estuaries are an increasing number of pleasure and ocean-going boats from other areas of Australia or overseas.

B1.3.3 System inputs

Animals

Animals in estuarine environments include cultured or wild fish, molluscs, crustaceans, annelids, polychaetes, and myriad other benthic invertebrates and migratory birds. Fish and shellfish may occasionally escape from semi-open and even semi-closed systems, particularly during flood events, or equipment and plumbing failure. Some states and territories stock species in estuaries, including barramundi, mulloway, whiting and prawns, to enhance recreational fishing.

Water

Water inputs to estuarine areas include natural river and tidal flows, as well as anthropogenic sources, such as ballast water, stormwater, sewage (treated or overflow) and agricultural runoff.

Other

Other influences on inputs to estuarine areas include:

• 
  aquaculture feeds, fish products, bait and berley
  
• 
  rubbish dumping
  
• 
  recreational boating inputs (e.g. weeds, water and mud brought in on trailers)
  
• 
  processing waste from fish
  
• 
  people.
  

Large numbers of people, from a wide variety of backgrounds, work in and enjoy estuarine areas.

B1.3.4 System outputs

Animals

Estuarine animals include fish, molluscs, crustaceans, echinoderms and birds.

Water

Water includes tidal flows and river flows.

Other

Other influences on outputs from estuarine areas include:

• 
  ballast water uptake
  
• 
  recreational boating (residual water in boats)
  
• 
  dredging, and associated spoil and sediment
  
• 
  people
  
• 
  movement of boats from estuaries, either by water or over land, by commercial and recreational users.
  

B1.3.5 Groups involved

The groups involved in management of estuaries vary by jurisdiction. They are likely to include local authorities, port authorities, local government agencies, and state or territory departments (such as lands, national parks, fisheries and environmental protection agencies).

B1.3.6 Legislation and codes of practice

Legislation relating to the management of estuary fisheries is generally managed by state and territory fisheries managers. The exceptions are fisheries that are managed under the Environment Protection and Biodiversity Conservation Act 1999 by the Australian Government Department of the Environment, and marine parks with estuarine components that are managed under national parks legislation. The Recfish National Code of Practice for Recreational and Sport Fishing (recfishingresearch.org/national-code-of-practice) applies in all environments.

Marine aquaculture legislation may need to be considered. This generally falls under state and territory fisheries departments.

Many ports operate under Commonwealth legislation rather than state or territory legislation. Some estuaries are administered by the Australian Government Department of Defence or have significant input from Aboriginal lands councils.

See Appendix 1 for information on relevant legislation.

B1.3.7 Occupational health

Immunocompromised people may be vulnerable to bacterial (e.g. Vibrio vulnificus) infections in estuarine areas. Some highly toxic dinoflagellates are also associated with estuarine environments. See Section B1.2.7 and Appendix 2 for information on seafood-borne disease in humans.

B1.4 Marine

Fisheries in open ocean waters include both motile and sessile wild-catch industries, fish and shellfish ranching sectors, net-pen aquaculture industries, and fisheries based on restocking and reseeding of finfish and molluscs. Within these sectors, there are large variations in the degree of mobility of species. As a result, development of effective emergency management plans requires specific information on each species and industry.

Motile species in coastal and open oceanic systems include a variety of commercially important wild-catch finfish (e.g. tuna, mackerel, reef fish, whiting, bream, mulloway, snapper), wild-catch prawns (Haliporoides, Penaeus and Metapenaeus species), other crustaceans (e.g. rock lobsters, crabs, bugs) and cephalopods (e.g. cuttlefish, squid, octopus), as well as a large number of non-commercially or recreationally important fish and crustaceans.

Sedentary species, or those of limited mobility, include abalone, marine snails, scallops, edible bivalves and pearl oyster species.

B1.4.1 Practices

Enterprises in marine and coastal areas are fishing commercially and recreationally for molluscs, crustaceans, cephalopods and finfish. The types of equipment and techniques used to target these species vary.

Aquaculture husbandry practices and the management of stock, broodstock selection, hatchery management and biodiversity may be issues to consider when restocking, ranching and reseeding practices occur in open waters. However, the occasional escape of stock from grow-out aquaculture enterprises can raise concerns over management of genetics, because inbred fish may be weaker and more susceptible to diseases. Once the stock is released into the environment, this section of the manual is relevant, and the principles for managing disease in wild stocks should be applied.

Aquaculture industries often source broodstock, and sometimes larvae, from the wild marine fisheries to support enterprises producing finfish, crustaceans and molluscs.

In wild-catch fisheries, the criteria used for selecting stocks for harvest should be considered. For the most mobile species, stocks selected for harvest will usually be the significant stocks. In the abalone industry, for example, quotas are allocated to larger areas, but the specific microenvironments harvested tend to be those with the best (or most accessible) populations. Populations in areas of low recruitment tend to be under-represented and underused because of the extra fishing effort required. Therefore, pressure is applied to the higher-density populations. This can affect a disease control exercise, as it can result in skewed data if commercial catches are used for surveillance purposes.

In the pearling industry, there has been a shift, since the 1950s, away from wild harvest of pearl oysters towards their culturing. Quotas are now set on the number of pearl oysters that can be taken from the wild and transported to farms for culture. In addition, pearl oyster spat are now also produced in hatcheries.

B1.4.2 Premises and equipment

In general terms, wild-catch harvesting of pelagic and demersal species of marine and estuarine finfish occurs by trawl, seine, longline, diving, set net, trap, and rod and line. This gear is mainly constructed of nylon, hemp, and galvanised or stainless steel. Divers taking pearl oysters generally dive by hookah and wear drysuits composed of neoprene, or nylon and urethane. They place the oysters into netting bags and send these up on lines to the boat on the surface.

If gear is used to catch diseased fish from one area, consideration must be given to the likelihood of transmission of the disease agent if the gear is then used in another area. Transmissibility of the disease agent depends on its properties. The fishing gear can be heavily contaminated with biological material (e.g. fish scales and mucus on nets, and mud on otter/trawl boards, which help keep the mouth of a net open), so consideration should be given to cleaning and disinfection routines before the gear is used in another, disease-free area. For example, abalone herpesvirus can be transmitted on contaminated abalone diver equipment such as boat surfaces, nets and wetsuits. In the United Kingdom, used oyster culture equipment was implicated in the introduction of oyster herpesvirus from infected areas of mainland Europe. Protocols have been developed for cleaning and disinfecting such equipment before it is used in other areas.

Trawl, seine or set net, trap or line gear is used by trawlers and other purpose-built fishing vessels in the oceanic environment. Ocean-going fishing vessels tend to be larger than recreational craft (ranging from 5 m for inshore vessels to 100 m for the larger international vessels), are generally designed to be very seaworthy, and provide a good work platform.

Recreational fishers tend to be highly mobile, and the same gear or boats may be used in several areas within a relatively short time. Boats, lines, pots, nets, bait and berley are all part of the recreational fisher’s kit and can be sources of disease transmission between areas.

B1.4.3 System inputs

Animals

In the marine environment, the main input of live animals is migratory fish, escape of fish from semi-open aquaculture systems, migratory birds, marine mammals and humans. Some fish from stocking programmes in estuarine environments may travel into marine environments, and some species have been directly restocked into marine environments—for example, under the New South Wales Department of Primary Industry’s (NSW DPI’s) mulloway stocking programme in Botany Bay. Abalone and scallops have also been part of reseeding operations in marine areas in New South Wales and Queensland, respectively.

Water

Some potential sources of introduction of exotic pathogens into the marine environment are:

• 
  effluent from aquaculture activities
  
• 
  catchment and estuarine drainage
  
• 
  ballast water discharge
  
• 
  oceanic currents
  
• 
  bait.
  

Natural and artificial baits are used in the marine environment and can vary depending on the species targeted. They can be locally sourced or imported. Records documenting the source of any bait or feed used would be useful to determine whether such products could carry disease agents. Particular attention should be paid to imported products that could potentially carry exotic disease agents.

Personnel

Personnel in marine environments include:

• 
  recreational fishers
  
• 
  commercial fishers
  
• 
  divers
  
• 
  other users who may not come into direct contact with fish stocks, such as recreational boaters.
  

Equipment

Equipment used in the marine environment may include:

• 
  boats and other recreational watercraft (e.g. canoes, surf skis, jet skis)
  
• 
  nets
  
• 
  diving equipment, including wetsuits, drysuits and hookah apparatus
  
• 
  fishing equipment used by commercial and recreational fishers.
  

Other influences

Other influences on inputs to the marine environment include:

• 
  trawler movement and activities, such as dumping of catch or bycatch
  
• 
  processing plants at shore margins.
  

B1.4.4 System outputs

Animals—primary product

AFMA and state or territory fisheries departments maintain databases of fishing effort and catch records for their jurisdictions. Commercial fishing cooperatives may also maintain records of fishing effort and catch data.

The primary products are dead fish and invertebrates for processing on shore or at shore margins, and live animals for processing or sale as live animals (including to export markets). In future, there may be an increasing output of wild-caught live animals for grow-out in aquaculture and value-adding situations; these animals could potentially be grown out at a distance from the original site of harvest.

Water

There is no control over water distribution in the marine environment. Pathogen spread can be affected by tides and currents.

Vehicles and equipment

Machinery and vehicles are likely to be moved into and out of the area. Such movement needs to be considered if the vehicles are likely to contact other stock, potentially acting as a fomite for disease transmission.

Other

Controls are needed on the following waste products:

• 
  processing plant wastes
  
• 
  shipping operation wastes
  
• 
  ballast water.
  

In addition, education is needed on disposal of fishers’ refuse.

B1.4.5 Groups involved

Government groups vary between jurisdictions. They include primary industries departments (agriculture and/or fisheries), environmental protection agencies, marine parks authorities and water authorities. Other groups include commercial fishers, recreational fishers, aquaculture grow-out operators and conservationists. International regulations, international fisheries efforts in Australian waters and bycatch issues also need to be considered.

When considering industry groups for consultation in a marine and coastal open-water environment, all groups that depend on the environment, and those with a strong interest, should be identified—this includes groups representing fishing, aquaculture, tourism, local coastal residents, recreational groups, and health and environmental interests.

The fishing industry organisations for commercial species are grouped under the Management Advisory Committees, which report to the state and territory fisheries departments on those fisheries that are in state waters, or have been ceded to the states under the Off-shore Constitutional Settlement Agreement. The Management Advisory Committees for Commonwealth-managed fisheries report through AFMA. The fishing industry is represented at the state and national levels by industry associations (e.g. Tasmanian Fishing Industry Council). The key national agency is Seafood Services Australia. This body has an elected industry board, and its membership includes the major sectors of the commercial industry.

The Australian aquaculture industry is represented by the National Aquaculture Council and industry groups such as the Tasmanian Salmonid Growers Association, the Australian Prawn Farmers Association, the Tuna Boat Owners Association, the South Australian Oyster Growers Association and the Australian Barramundi Farmers Association. These are key groups to consult with if disease occurs in, or can affect, their farming sector.

B1.4.6 Legislation and codes of practice

Each state and territory has its own legislation consistent with its constitutional responsibility for managing animal health within its borders. National guidelines cover a number of areas of aquatic animal health management, and provide a national framework and guidance for development of jurisdiction-specific policies.

See Appendix 1 for information on relevant legislation for each jurisdiction and the Commonwealth, as well as some codes of practice.

B1.4.7 Occupational health

In general, the risks to consumers from open ocean environments are low. Inshore areas may have higher risks due to interaction with human waste systems, which can result in high levels of human pathogens in filter-feeding molluscs, and high metal or dioxin levels in both molluscs and finfish. Finfish generally show low retention of human enteric bacteria, except for transient loading after recent exposure. Filter feeders may accumulate algal toxins, causing conditions such as paralytic shellfish poisoning. This is usually rare in other species; however, ciguatoxin accumulates in some reef fish that are higher in the food chain. Scombrotoxicosis from inappropriately handled tuna and mackerel is another uncommon human health problem.

See Appendix 2 for information on seafood-borne disease in humans.

The working environment

The ocean can be an extremely hostile environment, especially to inexperienced or poorly equipped workers. Death by drowning is one risk. Pearl and abalone divers are also exposed to the risk of shark attacks and decompression illness.